[2023-03-18 23:14:12,696] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:14:12,696] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:14:12,696] [INFO] DQC Reference Directory: /var/lib/cwl/stg82e25df2-db81-494a-8c9c-fe0deb3ac050/dqc_reference
[2023-03-18 23:14:13,798] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:14:13,799] [INFO] Task started: Prodigal
[2023-03-18 23:14:13,799] [INFO] Running command: cat /var/lib/cwl/stg9434ad27-0e75-486b-b762-8061264de600/OceanDNA-b36644.fa | prodigal -d OceanDNA-b36644/cds.fna -a OceanDNA-b36644/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:14:22,703] [INFO] Task succeeded: Prodigal
[2023-03-18 23:14:22,704] [INFO] Task started: HMMsearch
[2023-03-18 23:14:22,704] [INFO] Running command: hmmsearch --tblout OceanDNA-b36644/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg82e25df2-db81-494a-8c9c-fe0deb3ac050/dqc_reference/reference_markers.hmm OceanDNA-b36644/protein.faa > /dev/null
[2023-03-18 23:14:22,868] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:14:22,868] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg9434ad27-0e75-486b-b762-8061264de600/OceanDNA-b36644.fa]
[2023-03-18 23:14:22,884] [INFO] Query marker FASTA was written to OceanDNA-b36644/markers.fasta
[2023-03-18 23:14:22,885] [INFO] Task started: Blastn
[2023-03-18 23:14:22,885] [INFO] Running command: blastn -query OceanDNA-b36644/markers.fasta -db /var/lib/cwl/stg82e25df2-db81-494a-8c9c-fe0deb3ac050/dqc_reference/reference_markers.fasta -out OceanDNA-b36644/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:14:23,385] [INFO] Task succeeded: Blastn
[2023-03-18 23:14:23,386] [INFO] Selected 21 target genomes.
[2023-03-18 23:14:23,387] [INFO] Target genome list was writen to OceanDNA-b36644/target_genomes.txt
[2023-03-18 23:14:23,400] [INFO] Task started: fastANI
[2023-03-18 23:14:23,400] [INFO] Running command: fastANI --query /var/lib/cwl/stg9434ad27-0e75-486b-b762-8061264de600/OceanDNA-b36644.fa --refList OceanDNA-b36644/target_genomes.txt --output OceanDNA-b36644/fastani_result.tsv --threads 1
[2023-03-18 23:14:36,917] [INFO] Task succeeded: fastANI
[2023-03-18 23:14:36,917] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg82e25df2-db81-494a-8c9c-fe0deb3ac050/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:14:36,917] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg82e25df2-db81-494a-8c9c-fe0deb3ac050/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:14:36,926] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:14:36,926] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 23:14:36,926] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Alcanivorax pacificus	strain=W11-5	GCA_000299335.2	1306787	1306787	type	True	78.6107	145	399	95	below_threshold
Alcanivorax indicus	strain=SW127	GCA_003259185.1	2202653	2202653	type	True	78.0739	122	399	95	below_threshold
Alcanivorax profundimaris	strain=ST75FaO-1	GCA_015265435.1	2735259	2735259	type	True	77.9703	115	399	95	below_threshold
Alcanivorax gelatiniphagus	strain=MEBiC 08158	GCA_005938655.1	1194167	1194167	type	True	77.6626	121	399	95	below_threshold
Alcanivorax limicola	strain=JB21	GCA_019931215.1	2874102	2874102	type	True	77.6556	105	399	95	below_threshold
Alcanivorax marinus	strain=R8-12	GCA_025532125.1	1177169	1177169	type	True	77.6277	121	399	95	below_threshold
Alcanivorax hongdengensis	strain=A-11-3	GCA_000300995.1	519051	519051	type	True	77.5095	113	399	95	below_threshold
Alcanivorax balearicus	strain=MACL04	GCA_025532145.1	413232	413232	type	True	77.4287	87	399	95	below_threshold
Alcanivorax xenomutans	strain=JC109	GCA_900217905.1	1094342	1094342	type	True	77.2366	84	399	95	below_threshold
Alcanivorax mobilis	strain=MT13131	GCA_002864685.1	2019569	2019569	type	True	77.1786	101	399	95	below_threshold
Stutzerimonas degradans	strain=FDAARGOS_876	GCA_016028635.1	2968968	2968968	suspected-type	True	76.6146	57	399	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	76.5342	70	399	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	76.4164	72	399	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 23:14:36,926] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36644/tc_result.tsv
[2023-03-18 23:14:36,926] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:14:36,926] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:14:36,926] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg82e25df2-db81-494a-8c9c-fe0deb3ac050/dqc_reference/checkm_data
[2023-03-18 23:14:36,927] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:14:36,931] [INFO] Task started: CheckM
[2023-03-18 23:14:36,931] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36644/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36644/checkm_input OceanDNA-b36644/checkm_result
[2023-03-18 23:15:05,113] [INFO] Task succeeded: CheckM
[2023-03-18 23:15:05,114] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.42%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 23:15:05,130] [INFO] ===== Completeness check finished =====
[2023-03-18 23:15:05,130] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:15:05,130] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36644/markers.fasta)
[2023-03-18 23:15:05,131] [INFO] Task started: Blastn
[2023-03-18 23:15:05,131] [INFO] Running command: blastn -query OceanDNA-b36644/markers.fasta -db /var/lib/cwl/stg82e25df2-db81-494a-8c9c-fe0deb3ac050/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36644/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:15:05,751] [INFO] Task succeeded: Blastn
[2023-03-18 23:15:05,752] [INFO] Selected 15 target genomes.
[2023-03-18 23:15:05,752] [INFO] Target genome list was writen to OceanDNA-b36644/target_genomes_gtdb.txt
[2023-03-18 23:15:05,762] [INFO] Task started: fastANI
[2023-03-18 23:15:05,763] [INFO] Running command: fastANI --query /var/lib/cwl/stg9434ad27-0e75-486b-b762-8061264de600/OceanDNA-b36644.fa --refList OceanDNA-b36644/target_genomes_gtdb.txt --output OceanDNA-b36644/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:15:14,370] [INFO] Task succeeded: fastANI
[2023-03-18 23:15:14,378] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 23:15:14,378] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_000299335.2	s__Alcanivorax_A pacificus	78.6107	145	399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013823245.1	s__Alcanivorax_A sp013823245	78.1574	120	399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259185.1	s__Alcanivorax_A indicus	78.0739	122	399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015265435.1	s__Alcanivorax profundimaris	77.9703	115	399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	97.49	97.23	0.85	0.77	11	-
GCF_009846755.1	s__Alcanivorax_A sp009846755	77.9417	126	399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016906305.1	s__Alcanivorax marinus_B	77.8105	127	399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005938655.1	s__Alcanivorax gelatiniphagus	77.6362	122	399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	98.53	98.53	0.93	0.93	3	-
GCF_000300995.1	s__Alcanivorax hongdengensis	77.5095	113	399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002864685.1	s__Alcanivorax mobilis	77.1786	101	399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	98.57	98.57	0.96	0.96	2	-
GCF_017589465.1	s__Pseudomonas sp017589465	76.7193	72	399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016919445.1	s__Pseudomonas sp016919445	76.5356	60	399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 23:15:14,378] [INFO] GTDB search result was written to OceanDNA-b36644/result_gtdb.tsv
[2023-03-18 23:15:14,378] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:15:14,380] [INFO] DFAST_QC result json was written to OceanDNA-b36644/dqc_result.json
[2023-03-18 23:15:14,380] [INFO] DFAST_QC completed!
[2023-03-18 23:15:14,380] [INFO] Total running time: 0h1m2s